Transcript biodiversity-DongJinKIM.pptx

Molecular Biodiversity of the Plant in Africa,
beyond the DNA Barcoding
Dong- Jin Kim
Nelson Mandela African Institute
of Science and Technology
Arusha, Tanzania
PRAGMA 23, Biodivesrity Workshop
Kunkuk Univ., Seoul., KOREA, Oct. 9 -12, 2012
The Biodiversity and Tourist Industry
around Arusha (contd)
The Biodiversity and Tourist Industry
around Arusha (contd)
Mountain Kilimanjaro, the Highest
Mountain in Africa, 5,895 m
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Mountain Kilimanjaro, the Highest
Mountain in Africa, 5,895 m (contd)
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Biodiversity:
Article 2 of the Convention of Biological Diversity (CBD) provides a short
description of the term `biodiversity', which refers essentially to the
diversity of living organisms, the genes they contain, and the communities
to which they contribute.
Three Levels of Biodiversity
Ecosystem Diversity :
the least-understood, trying to understand all the species in an ecosystem
and how they affect each other and their surroundings while at the same
time being affected themselves, is extremely complex
Species Diversity :
Most studies, either theoretical or experimental, focus on the species level,
as it is the easiest to work on both conceptually and in practice.
DNA barcoding is the molecular approach for the species diversity.
Genetic Diversity : Genetic diversity is the variety present at the level of
genes. Genes, made of DNA, are the building blocks that determine how an
organism will develop and what its traits and abilities will be. This level of
diversity can differ by alleles, by entire genes, or by units larger than genes
such as chromosomal structure.
Chemical diversity
DNA barcoding:
- An international consortium, the ‘Barcode of Life Initiative’
- identification of the estimated 10 million species on Earth.
- a diagnostic technique in which short DNA sequence(s)
Sample  DNA  PCR  sequencing  sequence analysis
DNA barcoding of the medicinal plants from Kenya and Tanzania
the herbal medicine powder  DNA analysis
useful for the standardization of the herbal medicines.
Nathi.seq
Olokunonoi.seq
Solanaceae
Mutongu .s eq
Oleisuki.seq
Othinguae.s eq
Entanyi_emburkel.s eq
Lamiaceae
Unknown1.s eq
Mubangi.s eq
Asteraceae
Muhuithia.seq
Mdaulia.seq
Entanyi_enkusero.s eq
Primulaceae
OlongÆututisho.s eq
Olkokola.s eq
Oloisuki.seq
Canellaceae
Ol-sogunoi.seq
Os okonoi.seq
Engangotisho.seq
Mdudu.s eq
Oloduay.seq
Orm umunyi.seq
Orm ukutan.seq
Fabaceae
enjani_lorpurkel.s eq
Elephant_stool.seq
Mwinu.s eq
muhenga.seq
Mukiduri.s eq
Shusiri_mwitu.s eq
Euphorbiaceae
Ludaha.seq
Orlopolosek.s eq
Orupande.seq
Anacardiaceae
Olungos wai.seq
Orbili.seq
Engomai.seq
Engamai.seq
Muhute.seq
Olchani_onyokie.s eq
gitunguru_kia_ngoma.s eq
Mugagatio.s eq
Amaryllidaceae
Gakungui.seq
Muiri.s eq
Muethia.seq
Watha.s eq
47.3
45
40
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30
25
20
15
Nucleotide Subs titutions (x100)
10
5
0
Legumes : Main Protein Source
Species relation
Genome relations
Lotus
Sesbania
Anthyllis
Galega
Vicia
Pisum
Melilotus
runcatula
Cicer
Medicago
sativa
Phaseolus
Vigna
Glycine
Cajanus
How can we put this genetic
variation to the improved variety,
and finally to the markers for
income increases??
An example of crop improvement program by molecular breeding, Cowpea
Genptyping by Sequencing
Striga in the maize field
an example of chemical ecology
Signaling for Haustorial dev.
Molecular biodiversity , Chemistry Approach
Ex). Phytochemistry of the whole plant extract of Striga
-
one of the most serious constraints to cereal crops
production in Africa
- has been used as a traditional medicine
HPLC chromatogram (280 nm)
Mass Spec profile
Major ions observed in LC-MS/MS analysis
Representitive FT-IR spectrum of
Yam samples (D. alata, D. dometorium)
D.alata
D.dometorium
PLS-DA score plot of Yam samples
(total 55 lines)
D. alata
D. bulbifera
D. cayenesis
D. dometorium
D. mangenotiana
D. prahensilis
D. rotundata
Genetic diversity of 342 yam
accessions base on SSR data
Dendrogram from PLS DA score plot
of Yam samples (total 63 lines)
D. rotundata
D. cayenesis
D. spp KN1
D. spp KE1
D. spp KG2
D. mangenotiana
D. spp KNK2
Dioscin
D. prahensilis
D. spp KNK4
D. spp KNK1
D. spp KG1
D. spp KE2
D. bulbifera
D. alata
Dioscin
D. dumetorium
D. batatas (Jangma)
D. japonica
(Sanma)
D.
opposita (Dunggunma)
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-
120 100 80
60
40
20
0
beyond DNA barcoding : Molecular Biodiversity
- Genomics
genome sequencing
High throughput processing
Metagenomics approach
Genome
Database
- Metabolomics
- Proteomics
Gene

protein
Chemiinformatics
Drug/compound

Bioinformatics
activity
Science & Technology Performance
– a function of Value-addition to Human Capital
Physical
Scientific research
R&D expenditure
Source: www.worldmapper.org
Patent registration
“… in the final analysis it is basically the mystery and utilization
of modern science and technology which distinguishes the South
from the North”. Abdus Salam African Nobel Laurete, 1979
Value addition to Human Capital – Finland & Korea, & LDC
Red = Post Primary, Blue = Post Secondary, Green = Post Tertiary
Source: World Bank, 2010
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African leaders (incl.
Nelson Mandela)
discussion with Jim
Wolfensohn
(then WB President),
2000/01.
Frannie Leautier,
then Vice President
of WBI, was given
the task of making
this happen.
Nelson Mandela greatly
concerned by the knowledge
gap (knowledge deficit) in SSA
suggested to Jim that Institutes
of S&T are perhaps Africa’s
single greatest need
(the likes of IITs & IISs in India).
Hippolyte Fofack, an
African WBI official, was
charged with developing
the concept in
collaboration with some
Africans in the Diaspora.
To provide the
best facilities for
graduate and
post-doc studies
and research
Objectives
of the AISTs
To catalyze the
development of
world class
science and
technology in
Africa
To bridge
between
research and
industrial
development
Technology parks
with incubators
and innovation
centres for spinoffs
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Structural Pillars of NM-AIST
ICT
Resource
Centre
NM AIST
Schools &
Departments
Technology
Park
(Incubators &
Innovation Centre)
Academia for Society
and Industry
Eco Park
(Botanicals, etc)
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NM-AIST
Is for research intensive graduate and post-doc
training in SET, viz. a Research University.
Its vision is to become a world-class institution
dedicated to the pursuit and promotion of excellence
in SET, and their applications for economic growth
and sustainable development.
Maintains strong national and
regional ownership.
Production of:
• Top-notch SET academics for higher learning
institutions;
• Competent researchers for R&D institutions;
• Techno-prenuers, industry captains, innovation
managers for stimulating, catalyzing and promoting
business start-ups and the growth of the local industry.
Establishment of a world-class environment for the
generation and application knowledge (through
research, innovation and technology development)
for wealth creation and sustainable development.
Life Sciences and Bioengineering (LSBE)
Biological
Engineering
Sustainable
Agriculture,
Plant and
Animal Biotech
Food Science
& Industrial
Biotechnology
Health and
Medical
Biosciences
Biodiversity
Conservation &
Management
Mathematics, Computational & Communication
Science & Engineering (MCCSE)
Information
Technology,
Development &
Management
Telecommunications
Systems &
Engineering
Information
Management &
Communication
Technology
Communication
Science &
Engineering
Mathematics &
Computational
Science
Computational
Science &
Engineering
Applied
Mathematics &
Computational
Engineering
Water & Environmental Science &
Engineering (WESE)
Environmental
Science
Hydrology and Water
Resources
Engineering
(HWRE)
Environmental Science
and Engineering
(EnSE)
Environmental
Engineering
Materials Science and Engineering (MaSE)
Sustainable Energy Science and Engineering
(SESE)
Business Studies and Humanities (BuSH)
•Management & Entrepreneurship
•Innovation Management
•Innovation Systems & Clusters
•IPR & Patent Management
Enterprise
Development &
Management
Communication
Skills & Research
Methodology
Philosophy,
Law & Ethics
Thank you very much !
Asanteni Sana !